Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1858 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0222727946 sf0222722077 2 22727946 3.81E-29 5.05E-25
vg0223976143 sf0223970274 2 23976143 3.87E-10 1.05E-07
vg0224242852 sf0224236983 2 24242852 2.59E-08 1.50E-07
vg0610459954 sf0610458955 6 10459954 3.28E-08 3.01E-07
vg0223720670 sf0223714801 2 23720670 3.48E-08 5.35E-08
vg0222634177 sf0222628308 2 22634177 5.75E-08 NA
vg0222858963 sf0222853094 2 22858963 1.07E-07 2.20E-06
vg0121117264 sf0121116219 1 21117264 1.34E-07 1.48E-06
vg0224869035 sf0224863166 2 24869035 3.53E-07 1.31E-06
vg1217651907 sf1217645862 12 17651907 1.04E-06 3.02E-06
vg1112606022 sf1112142225 11 12606022 9.06E-06 2.18E-06